BEAMing and Droplet Digital PCR Analysis of Mutant IDH1 mRNA in Glioma Patient Serum and Cerebrospinal Fluid Extracellular Vesicles

Development of biofluid-based molecular diagnostic tests for cancer is an important step towards tumor characterization and real-time monitoring in a minimally invasive fashion. Extracellular vesicles (EVs) are released from tumor cells into body fluids and can provide a powerful platform for tumor biomarkers because they carry tumor proteins and nucleic acids. Detecting rare point mutations in the background of wild-type sequences in biofluids such as blood and cerebrospinal fluid (CSF) remains a major challenge. Techniques such as BEAMing (beads, emulsion, amplification, magnetics) PCR and droplet digital PCR (ddPCR) are substantially more sensitive than many other assays for mutant sequence detection. Here, we describe a novel approach that combines biofluid EV RNA and BEAMing RT-PCR (EV-BEAMing), as well droplet digital PCR to interrogate mutations from glioma tumors. EVs from CSF of patients with glioma were shown to contain mutant IDH1 transcripts, and we were able to reliably detect and quantify mutant and wild-type IDH1 RNA transcripts in CSF of patients with gliomas. EV-BEAMing and EV-ddPCR represent a valuable new strategy for cancer diagnostics, which can be applied to a variety of biofluids and neoplasms

Preliminary Safety Criteria for Organic Watch List Tanks at the Hanford Site

Condensed-phase, rapid reactions of organic salts with nitrates/nitrites in Hanford High Level Radioactive Waste single-shell tanks could lead to structural failure of the tanks resulting in significant releases of radionuclides and toxic materials. This report establishes appropriate preliminary safety criteria to ensure that tank wastes will be maintained safe. These criteria show that if actual dry wastes contain less than 1.2 MJ/kg of reactants reaction energy or less 4.5 wt % of total organic carbon, then the waste will be safe and will not propagate if ignited. Waste moisture helps to retard reactions; when waste moisture exceeds 20 wt %, rapid reactions are prevented, regardless of organic carbon concentrations. Aging and degradation of waste materials has been considered to predict the types and amounts to organic compounds present in the waste. Using measurements of 3 waste phases (liquid, salt cake, and sludge) obtained from tank waste samples analyzed in the laboratory, analysis of variance (ANOVA) models were used to estimate waste states for unmeasured tanks. The preliminary safety criteria are based upon calorimetry and propagation testing of likely organic compounds which represent actual tank wastes. These included sodium salts of citrate, formate, acetate and hydroxyethylethylenediaminetricetate (HEDTA). Hot cell tests of actual tank wastes are planned for the future to confirm propagation tests performed in the laboratory. The effects of draining liquids from the tanks which would remove liquids and moisture were considered because reactive waste which is too dry may propagate. Evaporation effects which could remove moisture from the tanks were also calculated. The various ways that the waste could be heated or ignited by equipment failures or tank operations activities were considered and appropriate monitoring and controls were recommended

Outcomes of Surgical Treatment for Carcinoid Heart Disease: A Systematic Review and Meta-Analysis

Introduction and Objective: Carcinoid Heart Disease (CaHD) develops from vasoactive substances released by neuroendocrine tumors causing significant patient morbidity and mortality necessitating surgical intervention. We performed a systematic review and meta-analysis to elucidate granular perioperative details and long-term outcomes in these patients. Methods: Electronic search of Ovid, Scopus, Cumulative Index of Nursing and Allied Health Literature, and Cochrane Controlled Trials Register was performed. Nine articles comprising 416 patients who received surgery were selected. Primary outcomes investigated included patient characteristics, surgical characteristics and survival data. Study-level data were extracted and pooled for meta-analysis. Results: Primary outcomes consisted of survival, length of stay and thirty-day mortality. Secondary outcomes included presence of right heart failure pre-operatively and type of valve replaced. Right heart failure was present in 48%. Moderate or severe regurgitation was present in 97% of tricuspid and 72% of pulmonary valves. 99% of tricuspid and 59% of pulmonary valves were replaced. Mean hospital length of stay was 16 days. Thirty-day mortality was 9%. Mean follow up was 25 months. Median survival was 3 years. Conclusion: Surgical treatment of CaHD can be performed with acceptable short-term outcomes. However, overall survival appears to suffer from ongoing effects of the primary disease. Surgery is often performed after patients have extensive right-sided heart involvement. Overall, onset and duration of symptoms of carcinoid heart disease should be closely monitored to properly identify and refer patients who would most benefit from valvular surgery

Pleosporales

One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae

Highly frequent PIK3CA amplification is associated with poor prognosis in gastric cancer

<p>Abstract</p> <p>Background</p> <p>The phosphoinositide 3-kinase (PI3K)/Akt pathway plays a fundamental role in cell proliferation and survival in human tumorigenesis, including gastric cancer. <it>PIK3CA </it>mutations and amplification are two major causes of overactivation of this pathway in human cancers. However, until this work, there was no sound investigation on the association of <it>PIK3CA </it>mutations and amplification with clinical outcome in gastric cancer, particularly the latter.</p> <p>Methods</p> <p>Using direct sequencing and real-time quantitative PCR, we examined <it>PIK3CA </it>mutations and amplification, and their association with clinicopathological characteristics and clinical outcome of gastric cancer patients.</p> <p>Results</p> <p><it>PIK3CA </it>mutations and amplification were found in 8/113 (7.1%) and 88/131 (67%) gastric cancer patients, respectively. <it>PIK3CA </it>amplification was closely associated with increased phosphorylated Akt (p-Akt) level. No relationship was found between <it>PIK3CA </it>mutations and clinicopathological characteristics and clinical outcome in gastric cancer. <it>PIK3CA </it>amplification was significantly positively associated with cancer-related death. Importantly, Kaplan-Meier survival curves revealed that the patients with <it>PIK3CA </it>amplification had significantly shorter survival times than the patients without <it>PIK3CA </it>amplification.</p> <p>Conclusions</p> <p>Our data showed that <it>PIK3CA </it>mutations were not common, but its amplification was very common in gastric cancer and may be a major mechanism in activating the PI3K/Akt pathway in gastric cancer. Importantly, Kaplan-Meier survival curves revealed that <it>PIK3CA </it>amplification was significantly positively associated with poor survival of gastric cancer patients. Collectively, the PI3K/Akt signaling pathway may be an effective therapeutic target in gastric cancer.</p

Quantum Turbulence

The present article reviews the recent developments in the physics of quantum turbulence. Quantum turbulence (QT) was discovered in superfluid $^4$He in the 1950s, and the research has tended toward a new direction since the mid 90s. The similarities and differences between quantum and classical turbulence have become an important area of research. QT is comprised of quantized vortices that are definite topological defects, being expected to yield a model of turbulence that is much simpler than the classical model. The general introduction of the issue and a brief review on classical turbulence are followed by a description of the dynamics of quantized vortices. Then, we discuss the energy spectrum of QT at very low temperatures. At low wavenumbers, the energy is transferred through the Richardson cascade of quantized vortices, and the spectrum obeys the Kolmogorov law, which is the most important statistical law in turbulence; this classical region shows the similarity to conventional turbulence. At higher wavenumbers, the energy is transferred by the Kelvin-wave cascade on each vortex. This quantum regime depends strongly on the nature of each quantized vortex. The possible dissipation mechanism is discussed. Finally, important new experimental studies, which include investigations into temperature-dependent transition to QT, dissipation at very low temperatures, QT created by vibrating structures, and visualization of QT, are reviewed. The present article concludes with a brief look at QT in atomic Bose-Einstein condensates.Comment: 13 pages, 5 figures, Review article to appear in J. Phys. Soc. Jp

Mutational Analysis of EGFR and Related Signaling Pathway Genes in Lung Adenocarcinomas Identifies a Novel Somatic Kinase Domain Mutation in FGFR4

BACKGROUND: Fifty percent of lung adenocarcinomas harbor somatic mutations in six genes that encode proteins in the EGFR signaling pathway, i.e., EGFR, HER2/ERBB2, HER4/ERBB4, PIK3CA, BRAF, and KRAS. We performed mutational profiling of a large cohort of lung adenocarcinomas to uncover other potential somatic mutations in genes of this signaling pathway that could contribute to lung tumorigenesis. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed genomic DNA from a total of 261 resected, clinically annotated non-small cell lung cancer (NSCLC) specimens. The coding sequences of 39 genes were screened for somatic mutations via high-throughput dideoxynucleotide sequencing of PCR-amplified gene products. Mutations were considered to be somatic only if they were found in an independent tumor-derived PCR product but not in matched normal tissue. Sequencing of 9MB of tumor sequence identified 239 putative genetic variants. We further examined 22 variants found in RAS family genes and 135 variants localized to exons encoding the kinase domain of respective proteins. We identified a total of 37 non-synonymous somatic mutations; 36 were found collectively in EGFR, KRAS, BRAF, and PIK3CA. One somatic mutation was a previously unreported mutation in the kinase domain (exon 16) of FGFR4 (Glu681Lys), identified in 1 of 158 tumors. The FGFR4 mutation is analogous to a reported tumor-specific somatic mutation in ERBB2 and is located in the same exon as a previously reported kinase domain mutation in FGFR4 (Pro712Thr) in a lung adenocarcinoma cell line. CONCLUSIONS/SIGNIFICANCE: This study is one of the first comprehensive mutational analyses of major genes in a specific signaling pathway in a sizeable cohort of lung adenocarcinomas. Our results suggest the majority of gain-of-function mutations within kinase genes in the EGFR signaling pathway have already been identified. Our findings also implicate FGFR4 in the pathogenesis of a subset of lung adenocarcinomas

The effect of Spirulina sauce, as a functional food, on cardiometabolic risk factors, oxidative stress biomarkers, glycemic profile, and liver enzymes in nonalcoholic fatty liver disease patients:A randomized double-blinded clinical trial

OBJECTIVE: This study sought to investigate the effect of Spirulina on cardiometabolic risk factors, oxidative stress biomarkers, glycemic profile, and liver enzymes in nonalcoholic fatty liver disease (NAFLD) patients. METHODS: This randomized, double‐blind clinical trial was performed on 46 NAFLD patients. Subjects were allocated to consume either Spirulina sauce or placebo, each 20 g/day for 8 weeks. Fatty liver grade, liver enzymes, anthropometric parameters, blood pressure, and serum lipids, glucose, insulin, malondialdehyde, and antioxidant capacity were assessed pre‐ and postintervention. RESULTS: Fatty liver grade was significantly different between the two groups. A significant change for ALT (alanine aminotransferase) and AST (aspartate aminotransferase) was seen between the two groups (p = .03 and .02, respectively), while ALP (alkaline phosphatase) serum levels were not significantly different within or between groups. Pertaining to glycemic profile, all variables, except HOMA‐IR, were not significantly different within or between groups. Finally, statistically significant changes were seen in both MDA (malondialdehyde) and TAC (total antioxidant capacity) among the groups (p = .04 and <.001, respectively). CONCLUSIONS: Spirulina may improve fatty liver grade by modifying liver enzymes, oxidative stress, and some lipid profiles; however, there was effect of Spirulina on anthropometric characteristics and blood pressure

Mutations of PIK3CA in gastric adenocarcinoma

BACKGROUND: Activation of the phosphatidylinositol 3-kinase (PI3K) through mutational inactivation of PTEN tumour suppressor gene is common in diverse cancer types, but rarely reported in gastric cancer. Recently, mutations in PIK3CA, which encodes the p110α catalytic subunit of PI3K, have been identified in various human cancers, including 3 of 12 gastric cancers. Eighty percent of these reported mutations clustered within 2 regions involving the helical and kinase domains. In vitro study on one of the "hot-spot" mutants has demonstrated it as an activating mutation. METHODS: Based on these data, we initiated PIK3CA mutation screening in 94 human gastric cancers by direct sequencing of the gene regions in which 80% of all the known PIK3CA mutations were found. We also examined PIK3CA expression level by extracting data from the previous large-scale gene expression profiling study. Using Significance Analysis of Microarrays (SAM), we further searched for genes that show correlating expression with PIK3CA. RESULTS: We have identified PIK3CA mutations in 4 cases (4.3%), all involving the previously reported hotspots. Among these 4 cases, 3 tumours demonstrated microsatellite instability and 2 tumours harboured concurrent KRAS mutation. Data extracted from microarray studies showed an increased expression of PIK3CA in gastric cancers when compared with the non-neoplastic gastric mucosae (p < 0.001). SAM further identified 2910 genes whose expression levels were positively associated with that of PIK3CA. CONCLUSION: Our data suggested that activation of the PI3K signalling pathway in gastric cancer may be achieved through up-regulation or mutation of PIK3CA, in which the latter may be a consequence of mismatch repair deficiency